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- EMDB-3954: Cryo-EM structure of the human INO80 complex bound to nucleosome -

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Entry
Database: EMDB / ID: 3954
TitleCryo-EM structure of the human INO80 complex bound to nucleosome
Map datamap of human INO80 bound to nucleosome
SampleComplex of core human INO80 with nucleosome:
nucleosome / human INO80 / Histone subunits / RuvB-like 1 / RuvB-like 2 / DNA helicase INO80 / Actin-related protein 5 / Histone H3.1 / Histone H4 / Histone H2A type 1-B/E ...nucleosome / human INO80 / Histone subunits / RuvB-like 1 / RuvB-like 2 / DNA helicase INO80 / Actin-related protein 5 / Histone H3.1 / Histone H4 / Histone H2A type 1-B/E / Histone H2B type 1-J / INO80 complex subunit B / (nucleic-acidNucleic acid) x 2 / (ligand) x 2
Function / homologyDNA Damage Recognition in GG-NER / Core histone H2A/H2B/H3/H4 / INO80 complex, subunit Ies2 / DNA helicase Ino80 / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / RuvB-like helicase 1 / RuvB-like helicase 2 / SNF2-like, N-terminal domain superfamily ...DNA Damage Recognition in GG-NER / Core histone H2A/H2B/H3/H4 / INO80 complex, subunit Ies2 / DNA helicase Ino80 / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / RuvB-like helicase 1 / RuvB-like helicase 2 / SNF2-like, N-terminal domain superfamily / Actin / SNF2 family N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Helicase conserved C-terminal domain / RNA Polymerase I Chain Elongation / HIT zinc finger / PAPA-1-like conserved region / DNA-binding domain / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Actin-related protein 5 / RuvB-like / Histone H2B signature. / Actin family / Deposition of new CENPA-containing nucleosomes at the centromere / Histone H3/CENP-A / G2/M DNA damage checkpoint / SNF2-related, N-terminal domain / Histone H2B / Helicase, C-terminal / Histone H4 / Histone H2A / AAA+ ATPase domain / Actin, conserved site / DBINO domain / TATA box binding protein associated factor (TAF) / INO80 complex subunit B-like conserved region / RNA Polymerase I Promoter Opening / Histone H2A/H2B/H3 / Zinc finger, HIT-type / Histone-fold / TIP49, P-loop domain / Helicase superfamily 1/2, ATP-binding domain / Histone H4, conserved site / Histone H3 signature 1. / TIP49 P-loop domain / Actins signature 2. / B-WICH complex positively regulates rRNA expression / Factors involved in megakaryocyte development and platelet production / HDMs demethylate histones / HATs acetylate histones / RMTs methylate histone arginines / Histone H3 signature 2. / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / NoRC negatively regulates rRNA expression / SUMOylation of chromatin organization proteins / DNA methylation / PKMTs methylate histone lysines / Transcriptional regulation by small RNAs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Amyloid fiber formation / Chromatin modifying enzymes / Interleukin-7 signaling / Packaging Of Telomere Ends / Meiotic synapsis / Telomere Extension By Telomerase / DBINO domain profile. / HDACs deacetylate histones / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Pre-NOTCH Transcription and Translation / E3 ubiquitin ligases ubiquitinate target proteins / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / Estrogen-dependent gene expression / Meiotic recombination / negative regulation of estrogen receptor binding / positive regulation of nuclear cell cycle DNA replication / transcriptional activation by promoter-enhancer looping / positive regulation of telomerase RNA localization to Cajal body / histone H2A acetylation / nucleosome mobilization / regulation of transcription from RNA polymerase II promoter in response to stress / establishment of protein localization to chromatin
Function and homology information
SourceHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsAyala R / Willhoft O / Aramayo RJ / Wilkinson M / McCormack EA / Ocloo L / Wigley DB / Zhang X
CitationJournal: Nature / Year: 2018
Title: Structure and regulation of the human INO80-nucleosome complex.
Authors: Rafael Ayala / Oliver Willhoft / Ricardo J Aramayo / Martin Wilkinson / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley / Xiaodong Zhang
Validation ReportPDB-ID: 6hts

SummaryFull reportAbout validation report
DateDeposition: Oct 27, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Apr 25, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hts
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3954.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
270 pix
1.09 Å/pix.
= 294.3 Å
270 pix
1.09 Å/pix.
= 294.3 Å
270 pix
1.09 Å/pix.
= 294.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density
Contour Level:0.0155 (by author), 0.035 (movie #1):
Minimum - Maximum-0.036022097 - 0.11846963
Average (Standard dev.)0.00095604477 (0.0058174892)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 339.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z270270270
origin x/y/z0.0120.0120.012
length x/y/z294.300294.300294.300
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0680.1970.002

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Supplemental data

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Sample components

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Entire Complex of core human INO80 with nucleosome

EntireName: Complex of core human INO80 with nucleosome / Number of components: 17

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Component #1: protein, Complex of core human INO80 with nucleosome

ProteinName: Complex of core human INO80 with nucleosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, nucleosome

ProteinName: nucleosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, human INO80

ProteinName: human INO80 / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Histone subunits

ProteinName: Histone subunits / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, RuvB-like 1

ProteinName: RuvB-like 1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.296914 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, RuvB-like 2

ProteinName: RuvB-like 2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.222465 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #7: protein, DNA helicase INO80

ProteinName: DNA helicase INO80 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 146.390703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #8: protein, Actin-related protein 5

ProteinName: Actin-related protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.372336 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #9: protein, Histone H3.1

ProteinName: Histone H3.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.437167 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #10: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.165551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.935239 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, INO80 complex subunit B

ProteinName: INO80 complex subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.704172 kDa
SourceSpecies: synthetic construct (others)

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Component #14: nucleic-acid, DNA (142-MER)

Nucleic-acidName: DNA (142-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG) (DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DC)(DT) (DC)(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DT)(DC)(DG)(DT)(DG) (DT)(DC)(DT)(DT)(DA)(DC)(DC)(DG)(DG)(DG) (DT)(DT)(DG)(DG)(DA)(DC)(DT)(DC)(DA)(DA) (DG)(DA)(DC)(DG)(DA)(DT)(DA)(DG)(DT)(DT) (DA)(DC)(DC)
MassTheoretical: 62.533809 kDa
SourceSpecies: synthetic construct (others)

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Component #15: nucleic-acid, DNA (142-MER)

Nucleic-acidName: DNA (142-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DT)(DA)(DA)(DC)(DT)(DA)(DT)(DC) (DG)(DT)(DC)(DT)(DT)(DG)(DA)(DG)(DT)(DC) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DA)(DC)(DT) (DT)(DA)(DT)(DC)(DG)(DC)(DC)(DA)(DC)(DC) (DC)(DC)(DG)(DA)(DG)(DT)(DA)(DC)(DA)(DT) (DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)
MassTheoretical: 61.897449 kDa
SourceSpecies: synthetic construct (others)

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Component #16: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #17: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 58145
3D reconstructionSoftware: RELION / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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